Behind the Scene
NOTE: This game seems to be no longer under active development. The author of the game, John Halter, has failed to provide continued updates on the development of the game and to forfill his obligations to the Kickstarter backers. The information below is provided for historic reasons. Most of the complexity of the game is in the simulated environment and simluated genetics engine which are hardly noticable while playing but make very important impacts on the game. This section of the is here to tell you about all the "behind the scenes" simulations which goes on while you play. 'Player Genome' All the traits of your bacteria in the game are based on a genome that bacterium has. This DNA, just like for real bacteria, is a string of nucleotides (A's T's C's and G's). This genome is about 3,000 nucleotides long made of genes around 15 nucleotides long. A gene is what a trait is based on. This gene, like in real life, starts with the codon "ATG" and ends in "TGA" (although in reality there are 3 stop codons; this game only uses one). The ATG is followed by a regulatory region which tells the computer what gene it is and how to handle the gene. After that are the nucleotides which will make the value of the gene. The computer reads the gene codon by codon, and gets a value from each codon – the values of the codons range from 0 to 60. These values are then entered into a mathematical formula, which is different for each gene. An example of a formula for a gene, is to average all the values of codons and have the resulting average represent the gene. The use of different formulas is to simulate the importance of different folding patterns and structural differences in a protein. This way different strings of nucleotides will produce different values and different evolutionary advantages depending on the gene. Copying the genome of your bacteria will introduce copy error mutations. These mutations are only point mutations (single base substitutions) and do not include insertion/deletion mutations. But the substitutions do occur similarly to real life where transition mutations (purine<-> purine or pyrimidine <-> pyrimidine) occur more common than transvertion mutations (purine<->pyrimidine). Silent mutations do happen where a nucleotide can change a codon, but doesn't change the resulting amino acid, thus having no effect on the protein or trait. All the above information also applies to the plasmids. There is also some "junk" DNA in every genome. 'Strain Name' Believe it or not, the Strain names in the micropedia are not randomly generated, but follow a couple of rules. These rules are based on how different strains were named in a lab John worked at in College. In this lab bacterial strains were named by 3 letters and a number. The first was the nutritional requirement of the bacteria, the second the pH the bacteria grows, and third the tempurature the bacteria grows. Then the number was given to differentiate strains with the same 3 letters. The game has the same system in place with a slight variation. Bacteria with the same strain name have the same traits. But when a bacteria with new traits arise, a new name is given. This name is : 1st letter – Size of bacteria, 2nd letter : pH range of bacteria, 3rd letter – tempurature range. Then the number is given to differentiate the same letters. 'Bacteria Genome' The bacteria around you also have their own genome which their traits are based on, but the way their genome works is a bit different. And their evolution is also drastically different as they do not have a human player controlling them. While each bacteria has it's own genome, those genomes are based on a set of stored species template genomes. In total there can be 800 different species of bacteria in the game, but not every species is simulated in the game at the same time. This is because your player is only near a few environments at a certain time, so species only found in those environments are simulated fully (species in other environments go thru a different simulation proccess). Ecology Each species has a rating for how common it is to see in a certain environment called Environmental dominance (ED). Species with a higher ED in an environment will be more likely to be seen by the player than species with a low ED. Bacteria can increase their ED by enough nutrients to 'survive', just as the player is required to collect nutrients to continue their species. An ED level can lower if a bacteria dies before collecting enough nutrients. If the total ED levels of all environments reach 0, the species has gone extinct, and all information is deleted. If the ED levels reach high enough (>100), the species can split into two species given that there aren't more than 800 species. Species Variation The genome of a species caries a template genome for all bacteria of that species, and it includes all variation of that species. This concept is called sub-species variation in the programming code. To save variation in a single string of nucleotides, the game uses degenerate bases – or one letter to represent two or more nucleotides. The degenerate bases are the same as the ones used in bioinformatics : R - A/G Y - C/T S - G/C W - A/T K - G/T M - A/C B - C/G/T D - A/G/T H - A/C/T V - A/C/G N - any So an example piece of DNA which is ARG could be AAG or AGG. But when the bacteria copies from the species template DNA, which version does it get? - At the begning, it's a 50-50 split (or if it has 3 nucleotides a 33-33-33 splite or 4 nucleotids 25-25-25-25 split). The game then tracks which bacteria have which variations, and tracks how well those bacteria are doing compared to the other variations. So if the AAG/AGG example started as a 50-50 split, but the AAG was giving an advantage to the bacteria with those variations, it might start shifting to a 60-40 split. Eventually the AAG variation will occur 100% of the time, and the degenerate base will be removed and the successful sequence will remain. This is how the same species of bacteria can have bacteria with different colors. When mutations are applied, they are applied to the species template genome. The mutation has the same properties as the players mutations (no in/del, transition vs transverstion rate), but when applied makes a degenerate base in the species template. So if the species template was AAG and a mutation of C happened in the 1st spot, the new code will be YAG. Now a subspet of bacteria will appear with this new mutation, and if they do well this mutation will be the dominant feature of the species. If it fails, it will disapper from the species. If it is neutral, Genetic Drift will take effect. Pre-Game Evolution Before you begin the game, the loading screen simulates evolution to provide you with a rich diversity of bacterial species to play with. The game starts with one base genome, and then applies mutations (single base pair) to this genome to diversify it into 800 unique copies. As the mutations are applied, the game tracks the relatedness between the bacteria and provides each species with numbers representing species,genus,family,order,class, and phylum taxonomic classifications. There is now a second round of modification, where each species,genus,family,order,class, and phylum recieves a name. And each species gets their genome modified again based on their genus,family,order, and class. A representative trait is then modified for each taxonimic level based on the name. While this step isn't entirely scientifically accurate, it makes taxonomically related bacteria more related, and species from different taxonomic groupings less related. It also adds some scientific accuracy, because species with actual taxonomic names share at least one trait with their real counter-parts. Also See : List of Taxonomic Names List of Genus Names